Search results for "Molecular interactions"

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

2017

Abstract: The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, co-chairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing, ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthe…

2021

Parvoviruses are small single-stranded (ss) DNA viruses, which replicate in the nucleoplasm and affect both the structure and function of the nucleus. The nuclear stage of the parvovirus life cycle starts at the nuclear entry of incoming capsids and culminates in the successful passage of progeny capsids out of the nucleus. In this review, we will present past, current, and future microscopy and biochemical techniques and demonstrate their potential in revealing the dynamics and molecular interactions in the intranuclear processes of parvovirus infection. In particular, a number of advanced techniques will be presented for the detection of infection-induced changes, such as DNA modification…

Efficiency of antidepressant drugs as monoamine reuptake inhibitors: analysis of the hydrophobicity influence using biopartitioning micellar chromato…

2004

The reuptake blockade of biogenic amines by antidepressants is related not only to their therapeutics effects, but also to their side effects and potential drug-drug interactions. As an alternative to classical quantitative structure-activity relationships studies, in this work we propose different quantitative retention-activity relationships (QRAR) models that are able to describe the monoamine reuptake inhibition by antidepressants. The retention of compounds is measured using a biopartitioning micellar chromatography (BMC) system that can simulate the same hydrophobic, electronic and steric molecular interactions as those that condition drug activity. Since all the compounds considered …

Magnetic Molecular Conductors Based on Bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF) and the Tris(chlorocyananilato)ferrate(III) Complex

2019

Electrocrystallization of the bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF) organic donor in the presence of the [Fe(ClCNAn)3]3– tris(chlorocyananilato)ferrate(III) paramagnetic anion in different stoichiometric ratios and solvent mixtures afforded two different hybrid systems formulated as [BEDT-TTF]4[Fe(ClCNAn)3]·3H2O (1) and [BEDT-TTF]5[Fe(ClCNAn)3]2·2CH3CN (2) (An = anilato). Compounds 1 and 2 present unusual structures without the typical segregated organic and inorganic layers, where layers of 1 are formed by Λ and Δ enantiomers of the anionic paramagnetic complex together with mixed-valence BEDT-TTF tetramers, while layers of 2 are formed by Λ and Δ enantiomers of the paramagnetic…

Novel σ1 antagonists designed for tumor therapy: Structure – activity relationships of aminoethyl substituted cyclohexanes

2021

Abstract Depending on the substitution pattern and stereochemistry, 1,3-dioxanes 1 with an aminoethyl moiety in 4-position represent potent σ1 receptor antagonists. In order to increase the stability, a cyclohexane ring first replaced the acetalic 1, 3-dioxane ring of 1. A large set of aminoethyl substituted cyclohexane derivatives was prepared in a six-step synthesis. All enantiomers and diastereomers were separated by chiral HPLC at the stage of the primary alcohol 7, and their absolute configuration was determined by CD spectroscopy. Neither the relative nor the absolute configuration had a large impact on the σ1 affinity. The highest σ1 affinity was found for cis-configured benzylamines…

Dissecting the packing forces in mixed perfluorocarbon/aromatic co-crystals

2021

We carried out a systematic evaluation of the packing forces in co-crystals featuring monoiodo- and diiodo-perfluoroalkanes and 1,2,4-oxadiazoles through single crystal X-ray diffraction and theoretical analysis. The molecules assemble via a combination of halogen bonding and specific dispersive interactions involving the perfluorinated units. We quantitatively elucidated the nature and strength of such interactions through solid-state calculations and Hirshfeld surface analysis. One of the co-crystals, formed by two monoiodoperfluorodecane molecules, the longest perfluorinated chain ever solved at the atomic level, allowed us to fully highlight the role of fluorous interactions.

Similarities and differences between crystal and enzyme environmental effects on the electron density of drug molecules

2021

Abstract The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low‐molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. Howeve…

Environmental Noise and Nonlinear Relaxation in Biological Systems

2012

We analyse the effects of environmental noise in three different biological systems: (i) mating behaviour of individuals of 'Nezara viridula' (L.) (Heteroptera Pentatomidae); (ii) polymer translocation in crowded solution; (iii) an ecosystem described by a Verhulst model with a multiplicative Lèvy noise. Specifically, we report on experiments on the behavioural response of 'N. viridula' individuals to sub-threshold deterministic signals in the presence of noise. We analyse the insect response by directionality tests performed on a group of male individuals at different noise intensities. The percentage of insects which react to the sub-threshold signal shows a non-monotonic behavior, charac…

Type III Secretion-Dependent Cell Cycle Block Caused in HeLa Cells by Enteropathogenic Escherichia coliO103

2001

ABSTRACT Rabbit enteropathogenic Escherichia coli (EPEC) O103 induces in HeLa cells an irreversible cytopathic effect characterized by the recruitment of focal adhesions, formation of stress fibers, and inhibition of cell proliferation. We have characterized the modalities of the proliferation arrest and investigated its underlying mechanisms. We found that HeLa cells that were exposed to the rabbit EPEC O103 strain E22 progressively accumulated at 4C DNA content and did not enter mitosis. A significant proportion of the cells were able to reinitiate DNA synthesis without division, leading to 8C DNA content. This cell cycle inhibition by E22 was abrogated in mutants lacking EspA, -B, and -D…

Supramolecular functionalization and concomitant enhancement in properties of Au25 clusters

2014

We present a versatile approach for tuning the surface functionality of an atomically precise 25 atom gold cluster using specific host-guest interactions between ?-cyclodextrin (CD) and the ligand anchored on the cluster. The supramolecular interaction between the Au25 cluster protected by 4-(t-butyl)benzyl mercaptan, labeled Au25SBB18, and CD yielding Au25SBB18�?�CDn (n = 1, 2, 3, and 4) has been probed experimentally using various spectroscopic techniques and was further analyzed by density functional theory calculations and molecular modeling. The viability of our method in modifying the properties of differently functionalized Au25 clusters is demonstrated. Besides modifying their optoe…